OpenMS  2.7.0
Classes | Public Types | List of all members
ReactionMonitoringTransition Class Reference

This class stores a SRM/MRM transition. More...

#include <OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h>

Inheritance diagram for ReactionMonitoringTransition:
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Collaboration diagram for ReactionMonitoringTransition:
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Classes

struct  NameLess
 Comparator by name. More...
 
struct  ProductMZLess
 Comparator by Product ion MZ. More...
 

Public Types

enum  DecoyTransitionType { UNKNOWN , TARGET , DECOY }
 
typedef TargetedExperimentHelper::Configuration Configuration
 
typedef TargetedExperimentHelper::RetentionTime RetentionTime
 
typedef TargetedExperimentHelper::TraMLProduct Product
 
typedef TargetedExperimentHelper::Prediction Prediction
 

Public Member Functions

Constructors and destructors
 ReactionMonitoringTransition ()
 default constructor More...
 
 ReactionMonitoringTransition (const ReactionMonitoringTransition &rhs)
 copy constructor More...
 
 ReactionMonitoringTransition (ReactionMonitoringTransition &&) noexcept
 Move constructor. More...
 
 ~ReactionMonitoringTransition () override
 destructor More...
 
ReactionMonitoringTransitionoperator= (const ReactionMonitoringTransition &rhs)
 assignment operator More...
 
ReactionMonitoringTransitionoperator= (ReactionMonitoringTransition &&rhs)
 move assignment operator More...
 
Accessors
void setName (const String &name)
 
const StringgetName () const
 
void setNativeID (const String &name)
 
const StringgetNativeID () const
 
void setPeptideRef (const String &peptide_ref)
 
const StringgetPeptideRef () const
 
void setCompoundRef (const String &compound_ref)
 
const StringgetCompoundRef () const
 
void setPrecursorMZ (double mz)
 sets the precursor mz (Q1 value) More...
 
double getPrecursorMZ () const
 get the precursor mz (Q1 value) More...
 
bool hasPrecursorCVTerms () const
 Returns true if precursor CV Terms exist (means it is safe to call getPrecursorCVTermList) More...
 
void setPrecursorCVTermList (const CVTermList &list)
 
void addPrecursorCVTerm (const CVTerm &cv_term)
 
const CVTermListgetPrecursorCVTermList () const
 Obtain the list of CV Terms for the precursor. More...
 
void setProductMZ (double mz)
 
double getProductMZ () const
 
int getProductChargeState () const
 
bool isProductChargeStateSet () const
 
void addProductCVTerm (const CVTerm &cv_term)
 
const std::vector< Product > & getIntermediateProducts () const
 
void addIntermediateProduct (Product product)
 
void setIntermediateProducts (const std::vector< Product > &products)
 
void setProduct (Product product)
 
const ProductgetProduct () const
 
bool hasPrediction () const
 Returns true if a Prediction object exists (means it is safe to call getPrediction) More...
 
void setPrediction (const Prediction &prediction)
 
void addPredictionTerm (const CVTerm &prediction)
 
const PredictiongetPrediction () const
 Obtain the Prediction object. More...
 
DecoyTransitionType getDecoyTransitionType () const
 Returns the type of transition (target or decoy) More...
 
void setDecoyTransitionType (const DecoyTransitionType &d)
 Sets the type of transition (target or decoy) More...
 
double getLibraryIntensity () const
 Returns the library intensity (ion count or normalized ion count from a spectral library) More...
 
void setLibraryIntensity (double intensity)
 Sets the library intensity (ion count or normalized ion count from a spectral library) More...
 
Retention time

Retention time set on transition level

Note
Retention time can be set on analyte level (peptide / compound level) or transition level – usually the retention time set here on transition level is ignored, therefore only use this if you have a good reason.
void setRetentionTime (RetentionTime rt)
 Sets the retention time on transition level. More...
 
const RetentionTimegetRetentionTime () const
 Gets the retention time on transition level. More...
 
Detecting transitions

Transitions used for detection of analyte

Detecting transitions represent the set of transitions of an assay that should be used to enable candidate peak group detection. Ideally they were observed and validated in previous experiments and have an associated library intensity.

For an overview, see Schubert OT et al., Building high-quality assay libraries for targeted analysis of SWATH MS data., Nat Protoc. 2015 Mar;10(3):426-41. doi: 10.1038/nprot.2015.015. Epub 2015 Feb 12. PMID: 25675208

bool isDetectingTransition () const
 
void setDetectingTransition (bool val)
 
Identifying transitions

Transitions used for differentiation between different analyte isomers (peptidoforms).

Identifying transitions represent the set of transitions of an assay that should be used for the independent identification of a candidate peak group (often in relation to another analyte isomer or peptidoform). These transitions could for example be site-determining transitions in a phospho-proteomic DIA experiment. These transitions will be scored independently of the detecting transitions.

bool isIdentifyingTransition () const
 
void setIdentifyingTransition (bool val)
 
Quantifying transitions

Transitions used for quantification

Quantifying transitions represent the set of transitions of an assay that should be used for the quantification of the peptide. This includes exclusion of e.g. interfered transitions (example: light/heavy peptide pairs isolated in the same swath window), that should not be used for quantification of the peptide.

bool isQuantifyingTransition () const
 
void setQuantifyingTransition (bool val)
 
Predicates
bool operator== (const ReactionMonitoringTransition &rhs) const
 equality operator More...
 
bool operator!= (const ReactionMonitoringTransition &rhs) const
 inequality operator More...
 
- Public Member Functions inherited from CVTermList
 CVTermList ()=default
 Defaults constructor. More...
 
 CVTermList (const CVTermList &)=default
 Copy constructor. More...
 
 CVTermList (CVTermList &&) noexcept
 Move constructor. More...
 
virtual ~CVTermList ()
 Destructor. More...
 
CVTermListoperator= (const CVTermList &rhs) &=default
 Assignment operator. More...
 
CVTermListoperator= (CVTermList &&) &=default
 Move assignment operator. More...
 
void setCVTerms (const std::vector< CVTerm > &terms)
 sets the CV terms More...
 
void replaceCVTerm (const CVTerm &cv_term)
 replaces the specified CV term More...
 
void replaceCVTerms (const std::vector< CVTerm > &cv_terms, const String &accession)
 replaces the specified CV terms using the given accession number More...
 
void replaceCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map)
 replaces all cv terms with a map (can be obtained via getCVTerms) More...
 
void consumeCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map)
 merges the given map into the member map, no duplicate checking More...
 
const Map< String, std::vector< CVTerm > > & getCVTerms () const
 returns the accession string of the term More...
 
void addCVTerm (const CVTerm &term)
 adds a CV term More...
 
bool operator== (const CVTermList &cv_term_list) const
 equality operator More...
 
bool operator!= (const CVTermList &cv_term_list) const
 inequality operator More...
 
bool hasCVTerm (const String &accession) const
 checks whether the term has a value More...
 
bool empty () const
 return true if no terms are available More...
 
- Public Member Functions inherited from MetaInfoInterface
 MetaInfoInterface ()
 Constructor. More...
 
 MetaInfoInterface (const MetaInfoInterface &rhs)
 Copy constructor. More...
 
 MetaInfoInterface (MetaInfoInterface &&) noexcept
 Move constructor. More...
 
 ~MetaInfoInterface ()
 Destructor. More...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 Assignment operator. More...
 
MetaInfoInterfaceoperator= (MetaInfoInterface &&) noexcept
 Move assignment operator. More...
 
bool operator== (const MetaInfoInterface &rhs) const
 Equality operator. More...
 
bool operator!= (const MetaInfoInterface &rhs) const
 Equality operator. More...
 
const DataValuegetMetaValue (const String &name, const DataValue &default_value=DataValue::EMPTY) const
 Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...
 
const DataValuegetMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
 Returns the value corresponding to an index, or a default value (default: DataValue::EMPTY) if not found. More...
 
bool metaValueExists (const String &name) const
 Returns whether an entry with the given name exists. More...
 
bool metaValueExists (UInt index) const
 Returns whether an entry with the given index exists. More...
 
void setMetaValue (const String &name, const DataValue &value)
 Sets the DataValue corresponding to a name. More...
 
void setMetaValue (UInt index, const DataValue &value)
 Sets the DataValue corresponding to an index. More...
 
void removeMetaValue (const String &name)
 Removes the DataValue corresponding to name if it exists. More...
 
void removeMetaValue (UInt index)
 Removes the DataValue corresponding to index if it exists. More...
 
void addMetaValues (const MetaInfoInterface &from)
 function to copy all meta values from one object to this one More...
 
void getKeys (std::vector< String > &keys) const
 Fills the given vector with a list of all keys for which a value is set. More...
 
void getKeys (std::vector< UInt > &keys) const
 Fills the given vector with a list of all keys for which a value is set. More...
 
bool isMetaEmpty () const
 Returns if the MetaInfo is empty. More...
 
void clearMetaInfo ()
 Removes all meta values. More...
 

Protected Member Functions

Comparator classes.

These classes implement binary predicates that can be used to compare two transitions with respect to their name.

void updateMembers_ ()
 
- Protected Member Functions inherited from MetaInfoInterface
void createIfNotExists_ ()
 Creates the MetaInfo object if it does not exist. More...
 

Protected Attributes

Attributes
String name_
 id, required attribute More...
 
String peptide_ref_
 Reference to a specific peptide. More...
 
String compound_ref_
 Reference to a specific compound. More...
 
double library_intensity_
 Intensity of the product (q3) ion (stored in CV Term 1001226 inside the <Transition> tag) More...
 
DecoyTransitionType decoy_type_
 specific properties of a transition (e.g. specific CV terms) More...
 
Subelements
double precursor_mz_
 A transition has exactly one precursor and it must supply the CV Term 1000827 (isolation window target m/z) More...
 
CVTermListprecursor_cv_terms_
 (Other) CV Terms of the Precursor (Q1) of the transition or target More...
 
Product product_
 Product (Q3) of the transition. More...
 
std::vector< Productintermediate_products_
 Intermediate product ion information of the transition when using MS3 or above (optional) More...
 
RetentionTime rts
 Information about predicted or calibrated retention time (optional) More...
 
Predictionprediction_
 Information about a prediction for a suitable transition using some software (optional) More...
 
std::bitset< 3 > transition_flags_
 
- Protected Attributes inherited from CVTermList
Map< String, std::vector< CVTerm > > cv_terms_
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 Pointer to the MetaInfo object (0 by default) More...
 

Additional Inherited Members

- Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistrymetaRegistry ()
 Returns a reference to the MetaInfoRegistry. More...
 

Detailed Description

This class stores a SRM/MRM transition.

This class is capable of representing a <Transition> tag in a TraML document completely and contains all associated information.

The default values for precursor m/z is 0.0 which indicates that it is uninitialized.

Member Typedef Documentation

◆ Configuration

◆ Prediction

◆ Product

◆ RetentionTime

Member Enumeration Documentation

◆ DecoyTransitionType

Enumerator
UNKNOWN 

Unknown type.

TARGET 

Target transition.

DECOY 

Decoy transition.

Constructor & Destructor Documentation

◆ ReactionMonitoringTransition() [1/3]

default constructor

◆ ReactionMonitoringTransition() [2/3]

copy constructor

◆ ReactionMonitoringTransition() [3/3]

Move constructor.

◆ ~ReactionMonitoringTransition()

destructor

Member Function Documentation

◆ addIntermediateProduct()

void addIntermediateProduct ( Product  product)

◆ addPrecursorCVTerm()

void addPrecursorCVTerm ( const CVTerm cv_term)

◆ addPredictionTerm()

void addPredictionTerm ( const CVTerm prediction)

◆ addProductCVTerm()

void addProductCVTerm ( const CVTerm cv_term)

◆ getCompoundRef()

const String& getCompoundRef ( ) const

◆ getDecoyTransitionType()

DecoyTransitionType getDecoyTransitionType ( ) const

Returns the type of transition (target or decoy)

◆ getIntermediateProducts()

const std::vector<Product>& getIntermediateProducts ( ) const

◆ getLibraryIntensity()

double getLibraryIntensity ( ) const

Returns the library intensity (ion count or normalized ion count from a spectral library)

◆ getName()

const String& getName ( ) const

◆ getNativeID()

const String& getNativeID ( ) const

◆ getPeptideRef()

const String& getPeptideRef ( ) const

◆ getPrecursorCVTermList()

const CVTermList& getPrecursorCVTermList ( ) const

Obtain the list of CV Terms for the precursor.

Note
You first need to check whether they exist using hasPrecursorCVTerms()

◆ getPrecursorMZ()

double getPrecursorMZ ( ) const

get the precursor mz (Q1 value)

Referenced by ChromatogramExtractor::prepareSpectra_().

◆ getPrediction()

const Prediction& getPrediction ( ) const

Obtain the Prediction object.

Note
You first need to check whether the object is accessible using hasPrediction()

◆ getProduct()

const Product& getProduct ( ) const

◆ getProductChargeState()

int getProductChargeState ( ) const

◆ getProductMZ()

double getProductMZ ( ) const

◆ getRetentionTime()

const RetentionTime& getRetentionTime ( ) const

Gets the retention time on transition level.

Stores a retention time on the level of an individual transition

Note
This is very likely not what you want, to set the retention time of an analyte use TargetedExperimentHelper::PeptideCompound::getRetentionTime()

◆ hasPrecursorCVTerms()

bool hasPrecursorCVTerms ( ) const

Returns true if precursor CV Terms exist (means it is safe to call getPrecursorCVTermList)

◆ hasPrediction()

bool hasPrediction ( ) const

Returns true if a Prediction object exists (means it is safe to call getPrediction)

◆ isDetectingTransition()

bool isDetectingTransition ( ) const

◆ isIdentifyingTransition()

bool isIdentifyingTransition ( ) const

◆ isProductChargeStateSet()

bool isProductChargeStateSet ( ) const

◆ isQuantifyingTransition()

bool isQuantifyingTransition ( ) const

◆ operator!=()

bool operator!= ( const ReactionMonitoringTransition rhs) const

inequality operator

◆ operator=() [1/2]

assignment operator

◆ operator=() [2/2]

move assignment operator

◆ operator==()

bool operator== ( const ReactionMonitoringTransition rhs) const

equality operator

◆ setCompoundRef()

void setCompoundRef ( const String compound_ref)

◆ setDecoyTransitionType()

void setDecoyTransitionType ( const DecoyTransitionType d)

Sets the type of transition (target or decoy)

◆ setDetectingTransition()

void setDetectingTransition ( bool  val)

◆ setIdentifyingTransition()

void setIdentifyingTransition ( bool  val)

◆ setIntermediateProducts()

void setIntermediateProducts ( const std::vector< Product > &  products)

◆ setLibraryIntensity()

void setLibraryIntensity ( double  intensity)

Sets the library intensity (ion count or normalized ion count from a spectral library)

◆ setName()

void setName ( const String name)

◆ setNativeID()

void setNativeID ( const String name)

◆ setPeptideRef()

void setPeptideRef ( const String peptide_ref)

◆ setPrecursorCVTermList()

void setPrecursorCVTermList ( const CVTermList list)

◆ setPrecursorMZ()

void setPrecursorMZ ( double  mz)

sets the precursor mz (Q1 value)

◆ setPrediction()

void setPrediction ( const Prediction prediction)

◆ setProduct()

void setProduct ( Product  product)

◆ setProductMZ()

void setProductMZ ( double  mz)

◆ setQuantifyingTransition()

void setQuantifyingTransition ( bool  val)

◆ setRetentionTime()

void setRetentionTime ( RetentionTime  rt)

Sets the retention time on transition level.

Stores a retention time on the level of an individual transition

Note
This is very likely not what you want, to set the retention time of an analyte use TargetedExperimentHelper::PeptideCompound::getRetentionTime()

◆ updateMembers_()

void updateMembers_ ( )
protected

Member Data Documentation

◆ compound_ref_

String compound_ref_
protected

Reference to a specific compound.

◆ decoy_type_

DecoyTransitionType decoy_type_
protected

specific properties of a transition (e.g. specific CV terms)

◆ intermediate_products_

std::vector<Product> intermediate_products_
protected

Intermediate product ion information of the transition when using MS3 or above (optional)

◆ library_intensity_

double library_intensity_
protected

Intensity of the product (q3) ion (stored in CV Term 1001226 inside the <Transition> tag)

◆ name_

String name_
protected

id, required attribute

◆ peptide_ref_

String peptide_ref_
protected

Reference to a specific peptide.

◆ precursor_cv_terms_

CVTermList* precursor_cv_terms_
protected

(Other) CV Terms of the Precursor (Q1) of the transition or target

◆ precursor_mz_

double precursor_mz_
protected

A transition has exactly one precursor and it must supply the CV Term 1000827 (isolation window target m/z)

◆ prediction_

Prediction* prediction_
protected

Information about a prediction for a suitable transition using some software (optional)

◆ product_

Product product_
protected

Product (Q3) of the transition.

◆ rts

RetentionTime rts
protected

Information about predicted or calibrated retention time (optional)

◆ transition_flags_

std::bitset<3> transition_flags_
protected

A set of flags to store information about the transition at hand (currently: detecting, identifying and quantifying)